# This is the control script for LAMMPS. Run LAMMPS on GPU
echo both
log 2.1_Initialize.out
#-------------------------------------------------------------------------------
# Stage 2.1: Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units real
boundary p p p
atom_style full
atom_modify map array
box tilt large
read_data structure.dat
pair_style reax/c NULL checkqeq no safezone 10.0 mincap 1000
pair_coeff * * parameters.dat N Si
variable R equal 0.00198722
variable sysvol equal vol
variable sysmass equal mass(all)/6.0221367e+023
variable sysdensity equal v_sysmass/v_sysvol/1.0e-24
variable coulomb equal ecoul+elong
variable etotal equal etotal
variable pe equal pe
variable ke equal ke
variable evdwl equal evdwl
variable epair equal epair
variable ebond equal ebond
variable eangle equal eangle
variable edihed equal edihed
variable eimp equal eimp
variable lx equal lx
variable ly equal ly
variable lz equal lz
variable Nthermo equal 0
variable cella equal lx
variable cellb equal sqrt(ly*ly+xy*xy)
variable cellc equal sqrt(lz*lz+xz*xz+yz*yz)
variable cellalpha equal acos((xy*xz+ly*yz)/(v_cellb*v_cellc))
variable cellbeta equal acos(xz/v_cellc)
variable cellgamma equal acos(xy/v_cellb)
variable p equal press
variable pxx equal pxx
variable pyy equal pyy
variable pzz equal pzz
variable pyz equal pyz
variable pxz equal pxz
variable pxy equal pxy
variable sxx equal -pxx
variable syy equal -pyy
variable szz equal -pzz
variable syz equal -pyz
variable sxz equal -pxz
variable sxy equal -pxy
variable fmax equal fmax
variable fnorm equal fnorm
variable time equal step*dt+0.000001
variable surfacetension equal 0.5*v_lz*(0.5*(v_sxx+v_syy)-v_szz)
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo_modify flush yes
#
# Set up the fixed and movable groups
#
group fixed id 1 16 17 32 33 48 49 64 65 80
group fixed id 81 96 97 112 113 128 129 144 145 160
group fixed id 161 176 177 192 193 208 209 224 225 240
group fixed id 241 256 257 272 273 288 289 304 305 320
group fixed id 321 336 337 352 353 368 369 384 385 400
group fixed id 401 416 417 432 433 448 449 464 465 480
group fixed id 481 496 497 512 513 528 529 544 545 560
group fixed id 561 576 577 592 593 608 609 624 625 640
group fixed id 641 656 657 672 673 688 689 704 705 720
group fixed id 721 736 737 752 753 768 769 784 785 800
group fixed id 801 816 817 832 833 848 849 864 865 880
group fixed id 881 896 897 912 913 928 929 944 945 960
group fixed id 961 976 977 992 993 1008 1009 1024 1025 1040
group fixed id 1041 1056 1057 1072 1073 1088 1089 1104 1105 1120
group fixed id 1121 1136 1137 1152 1153 1168 1169 1184 1185 1200
group fixed id 1201 1216 1217 1232 1233 1248 1249 1264 1265 1280
group fixed id 1281 1296 1297 1312 1313 1328 1329 1344 1345 1360
group fixed id 1361 1376 1377 1392 1393 1408 1409 1424 1425 1440
group fixed id 1441 1456 1457 1472 1473 1488 1489 1504 1505 1520
group fixed id 1521 1536 1537 1552 1553 1568 1569 1584 1585 1600
group fixed id 1601 1616 1617 1632 1633 1648 1649 1664 1665 1680
group fixed id 1681 1696 1697 1712 1713 1728 1729 1744 1745 1760
group fixed id 1761 1776 1777 1792 1793 1808 1809 1824 1825 1840
group fixed id 1841 1856 1857 1872 1873 1888 1889 1904 1905 1920
group fixed id 1921 1936 1937 1952 1953 1968 1969 1984 1985 2000
group fixed id 2001 2016 2017 2032 2033 2048 2049 2053 2054 2058
group fixed id 2059 2063 2064 2068 2069 2073 2074 2078 2079 2083
group fixed id 2084 2088 2089 2093 2094 2098 2099 2103 2104 2108
group fixed id 2109 2113 2114 2118 2119 2123 2124 2128 2129 2133
group fixed id 2134 2138 2139 2143 2144 2148 2149 2153 2154 2158
group fixed id 2159 2163 2164 2168 2169 2173 2174 2178 2179 2183
group fixed id 2184 2188 2189 2193 2194 2198 2199 2203 2204 2208
group fixed id 2209 2213 2214 2218 2219 2223 2224 2228 2229 2233
group fixed id 2234 2238 2239 2243 2244 2248 2249 2253 2254 2258
group fixed id 2259 2263 2264 2268 2269 2273 2274 2278 2279 2283
group fixed id 2284 2288 2289 2293 2294 2298 2299 2303 2304 2308
group fixed id 2309 2313 2314 2318 2319 2323 2324 2328 2329 2333
group fixed id 2334 2338 2339 2343 2344 2348 2349 2353 2354 2358
group fixed id 2359 2363 2364 2368 2369 2373 2374 2378 2379 2383
group fixed id 2384 2388 2389 2393 2394 2398 2399 2403 2404 2408
group fixed id 2409 2413 2414 2418 2419 2423 2424 2428 2429 2433
group fixed id 2434 2438 2439 2443 2444 2448 2449 2453 2454 2458
group fixed id 2459 2463 2464 2468 2469 2473 2474 2478 2479 2483
group fixed id 2484 2488 2489 2493 2494 2498 2499 2503 2504 2508
group fixed id 2509 2513 2514 2518 2519 2523 2524 2528 2529 2533
group fixed id 2534 2538 2539 2543 2544 2548 2549 2553 2554 2558
group fixed id 2559 2563 2564 2568 2569 2573 2574 2578 2579 2583
group fixed id 2584 2588 2589 2593 2594 2598 2599 2603 2604 2608
group fixed id 2609 2613 2614 2618 2619 2623 2624 2628 2629 2633
group fixed id 2634 2638 2639 2643 2644 2648 2649 2653 2654 2658
group fixed id 2659 2663 2664 2668 2669 2673 2674 2678 2679 2683
group fixed id 2684 2688 2689 2699 2700 2710 2711 2721 2722 2732
group fixed id 2733 2743 2744 2754 2755 2765 2766 2776 2777 2787
group fixed id 2788 2798 2799 2809 2810 2820 2821 2831 2832 2842
group fixed id 2843 2853 2854 2864 2865 2880 2881 2896 2897 2912
group fixed id 2913 2928 2929 2944 2945 2960 2961 2976 2977 2992
group fixed id 2993 3008 3009 3024 3025 3040 3041 3056 3057 3072
group fixed id 3073 3088 3089 3104 3105 3120 3121 3136 3137 3152
group fixed id 3153 3168 3169 3184 3185 3200 3201 3216 3217 3232
group fixed id 3233 3248 3249 3264 3265 3280 3281 3296 3297 3312
group fixed id 3313 3328 3329 3344 3345 3360 3361 3376 3377 3392
group fixed id 3393 3408 3409 3424 3425 3440 3441 3456 3457 3472
group fixed id 3473 3488 3489 3504 3505 3520 3521 3536 3537 3552
group fixed id 3553 3568 3569 3584 3585 3600 3601 3616 3617 3632
group fixed id 3633 3648 3649 3664 3665 3680 3681 3696 3697 3712
group fixed id 3713 3728 3729 3744 3745 3760 3761 3776 3777 3792
group fixed id 3793 3808 3809 3824 3825 3840 3841 3856 3857 3872
group fixed id 3873 3888 3889 3904 3905 3920 3921 3936 3937 3952
group fixed id 3953 3968 3969 3984 3985 4000 4001 4016 4017 4032
group fixed id 4033 4048 4049 4064 4065 4080 4081 4096 4097 4112
group fixed id 4113 4128 4129 4144 4145 4160 4161 4176 4177 4192
group fixed id 4193 4208 4209 4224 4225 4240 4241 4256 4257 4272
group fixed id 4273 4288 4289 4304 4305 4320 4321 4336 4337 4352
group fixed id 4353 4368 4369 4384 4385 4400 4401 4416 4417 4432
group fixed id 4433 4448 4449 4464 4465 4480 4481 4496 4497 4512
group fixed id 4513 4528 4529 4544 4545 4560 4561 4576 4577 4592
group fixed id 4593 4608 4609 4624 4625 4640 4641 4656
group movable subtract all fixed
compute sum_f1 movable reduce sum fx fy fz
variable sum_fx equal c_sum_f1[1]
variable sum_fy equal c_sum_f1[2]
variable sum_fz equal c_sum_f1[3]
uncompute thermo_temp
compute thermo_temp movable temp
#
# Subsets
#
group subset_N_atom id 4657
group subset_thermostat id 2 3 4 5 6 7 8 9 10 11
group subset_thermostat id 12 13 14 15 18 19 20 21 22 23
group subset_thermostat id 24 25 26 27 28 29 30 31 34 35
group subset_thermostat id 36 37 38 39 40 41 42 43 44 45
group subset_thermostat id 46 47 50 51 52 53 54 55 56 57
group subset_thermostat id 58 59 60 61 62 63 66 67 68 69
group subset_thermostat id 70 71 72 73 74 75 76 77 78 79
group subset_thermostat id 82 83 84 85 86 87 88 89 90 91
group subset_thermostat id 92 93 94 95 98 99 100 101 102 103
group subset_thermostat id 104 105 106 107 108 109 110 111 114 115
group subset_thermostat id 116 117 118 119 120 121 122 123 124 125
group subset_thermostat id 126 127 130 131 132 133 134 135 136 137
group subset_thermostat id 138 139 140 141 142 143 146 147 148 149
group subset_thermostat id 150 151 152 153 154 155 156 157 158 159
group subset_thermostat id 162 163 164 165 166 167 168 169 170 171
group subset_thermostat id 172 173 174 175 178 179 180 181 182 183
group subset_thermostat id 184 185 186 187 188 189 190 191 194 195
group subset_thermostat id 196 197 198 199 200 201 202 203 204 205
group subset_thermostat id 206 207 210 211 212 213 214 215 216 217
group subset_thermostat id 218 219 220 221 222 223 226 227 228 229
group subset_thermostat id 230 231 232 233 234 235 236 237 238 239
group subset_thermostat id 242 243 244 245 246 247 248 249 250 251
group subset_thermostat id 252 253 254 255 258 259 260 261 262 263
group subset_thermostat id 264 265 266 267 268 269 270 271 274 275
group subset_thermostat id 276 277 278 279 280 281 282 283 284 285
group subset_thermostat id 286 287 290 291 292 293 294 295 296 297
group subset_thermostat id 298 299 300 301 302 303 306 307 308 309
group subset_thermostat id 310 311 312 313 314 315 316 317 318 319
group subset_thermostat id 322 323 324 325 326 327 328 329 330 331
group subset_thermostat id 332 333 334 335 338 339 340 341 342 343
group subset_thermostat id 344 345 346 347 348 349 350 351 354 355
group subset_thermostat id 356 357 358 359 360 361 362 363 364 365
group subset_thermostat id 366 367 370 371 372 373 374 375 376 377
group subset_thermostat id 378 379 380 381 382 383 386 387 388 389
group subset_thermostat id 390 391 392 393 394 395 396 397 398 399
group subset_thermostat id 402 403 404 405 406 407 408 409 410 411
group subset_thermostat id 412 413 414 415 418 419 420 421 422 423
group subset_thermostat id 424 425 426 427 428 429 430 431 434 435
group subset_thermostat id 436 437 438 439 440 441 442 443 444 445
group subset_thermostat id 446 447 450 451 452 453 454 455 456 457
group subset_thermostat id 458 459 460 461 462 463 466 467 468 469
group subset_thermostat id 470 471 472 473 474 475 476 477 478 479
group subset_thermostat id 482 483 484 485 486 487 488 489 490 491
group subset_thermostat id 492 493 494 495 498 499 500 501 502 503
group subset_thermostat id 504 505 506 507 508 509 510 511 514 515
group subset_thermostat id 516 517 518 519 520 521 522 523 524 525
group subset_thermostat id 526 527 530 531 532 533 534 535 536 537
group subset_thermostat id 538 539 540 541 542 543 546 547 548 549
group subset_thermostat id 550 551 552 553 554 555 556 557 558 559
group subset_thermostat id 562 563 564 565 566 567 568 569 570 571
group subset_thermostat id 572 573 574 575 578 579 580 581 582 583
group subset_thermostat id 584 585 586 587 588 589 590 591 594 595
group subset_thermostat id 596 597 598 599 600 601 602 603 604 605
group subset_thermostat id 606 607 610 611 612 613 614 615 616 617
group subset_thermostat id 618 619 620 621 622 623 626 627 628 629
group subset_thermostat id 630 631 632 633 634 635 636 637 638 639
group subset_thermostat id 642 643 644 645 646 647 648 649 650 651
group subset_thermostat id 652 653 654 655 658 659 660 661 662 663
group subset_thermostat id 664 665 666 667 668 669 670 671 674 675
group subset_thermostat id 676 677 678 679 680 681 682 683 684 685
group subset_thermostat id 686 687 690 691 692 693 694 695 696 697
group subset_thermostat id 698 699 700 701 702 703 706 707 708 709
group subset_thermostat id 710 711 712 713 714 715 716 717 718 719
group subset_thermostat id 722 723 724 725 726 727 728 729 730 731
group subset_thermostat id 732 733 734 735 738 739 740 741 742 743
group subset_thermostat id 744 745 746 747 748 749 750 751 754 755
group subset_thermostat id 756 757 758 759 760 761 762 763 764 765
group subset_thermostat id 766 767 770 771 772 773 774 775 776 777
group subset_thermostat id 778 779 780 781 782 783 786 787 788 789
group subset_thermostat id 790 791 792 793 794 795 796 797 798 799
group subset_thermostat id 802 803 804 805 806 807 808 809 810 811
group subset_thermostat id 812 813 814 815 818 819 820 821 822 823
group subset_thermostat id 824 825 826 827 828 829 830 831 834 835
group subset_thermostat id 836 837 838 839 840 841 842 843 844 845
group subset_thermostat id 846 847 850 851 852 853 854 855 856 857
group subset_thermostat id 858 859 860 861 862 863 866 867 868 869
group subset_thermostat id 870 871 872 873 874 875 876 877 878 879
group subset_thermostat id 882 883 884 885 886 887 888 889 890 891
group subset_thermostat id 892 893 894 895 898 899 900 901 902 903
group subset_thermostat id 904 905 906 907 908 909 910 911 914 915
group subset_thermostat id 916 917 918 919 920 921 922 923 924 925
group subset_thermostat id 926 927 930 931 932 933 934 935 936 937
group subset_thermostat id 938 939 940 941 942 943 946 947 948 949
group subset_thermostat id 950 951 952 953 954 955 956 957 958 959
group subset_thermostat id 962 963 964 965 966 967 968 969 970 971
group subset_thermostat id 972 973 974 975 978 979 980 981 982 983
group subset_thermostat id 984 985 986 987 988 989 990 991 994 995
group subset_thermostat id 996 997 998 999 1000 1001 1002 1003 1004 1005
group subset_thermostat id 1006 1007 1010 1011 1012 1013 1014 1015 1016 1017
group subset_thermostat id 1018 1019 1020 1021 1022 1023 1026 1027 1028 1029
group subset_thermostat id 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039
group subset_thermostat id 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051
group subset_thermostat id 1052 1053 1054 1055 1058 1059 1060 1061 1062 1063
group subset_thermostat id 1064 1065 1066 1067 1068 1069 1070 1071 1074 1075
group subset_thermostat id 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085
group subset_thermostat id 1086 1087 1090 1091 1092 1093 1094 1095 1096 1097
group subset_thermostat id 1098 1099 1100 1101 1102 1103 1106 1107 1108 1109
group subset_thermostat id 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119
group subset_thermostat id 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131
group subset_thermostat id 1132 1133 1134 1135 1138 1139 1140 1141 1142 1143
group subset_thermostat id 1144 1145 1146 1147 1148 1149 1150 1151 1154 1155
group subset_thermostat id 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165
group subset_thermostat id 1166 1167 1170 1171 1172 1173 1174 1175 1176 1177
group subset_thermostat id 1178 1179 1180 1181 1182 1183 1186 1187 1188 1189
group subset_thermostat id 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199
group subset_thermostat id 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211
group subset_thermostat id 1212 1213 1214 1215 1218 1219 1220 1221 1222 1223
group subset_thermostat id 1224 1225 1226 1227 1228 1229 1230 1231 1234 1235
group subset_thermostat id 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245
group subset_thermostat id 1246 1247 1250 1251 1252 1253 1254 1255 1256 1257
group subset_thermostat id 1258 1259 1260 1261 1262 1263 1266 1267 1268 1269
group subset_thermostat id 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279
group subset_thermostat id 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291
group subset_thermostat id 1292 1293 1294 1295 1298 1299 1300 1301 1302 1303
group subset_thermostat id 1304 1305 1306 1307 1308 1309 1310 1311 1314 1315
group subset_thermostat id 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325
group subset_thermostat id 1326 1327 1330 1331 1332 1333 1334 1335 1336 1337
group subset_thermostat id 1338 1339 1340 1341 1342 1343 1346 1347 1348 1349
group subset_thermostat id 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359
group subset_thermostat id 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371
group subset_thermostat id 1372 1373 1374 1375 1378 1379 1380 1381 1382 1383
group subset_thermostat id 1384 1385 1386 1387 1388 1389 1390 1391 1394 1395
group subset_thermostat id 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405
group subset_thermostat id 1406 1407 1410 1411 1412 1413 1414 1415 1416 1417
group subset_thermostat id 1418 1419 1420 1421 1422 1423 1426 1427 1428 1429
group subset_thermostat id 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439
group subset_thermostat id 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451
group subset_thermostat id 1452 1453 1454 1455 1458 1459 1460 1461 1462 1463
group subset_thermostat id 1464 1465 1466 1467 1468 1469 1470 1471 1474 1475
group subset_thermostat id 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485
group subset_thermostat id 1486 1487 1490 1491 1492 1493 1494 1495 1496 1497
group subset_thermostat id 1498 1499 1500 1501 1502 1503 1506 1507 1508 1509
group subset_thermostat id 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519
group subset_thermostat id 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531
group subset_thermostat id 1532 1533 1534 1535 1538 1539 1540 1541 1542 1543
group subset_thermostat id 1544 1545 1546 1547 1548 1549 1550 1551 1554 1555
group subset_thermostat id 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565
group subset_thermostat id 1566 1567 1570 1571 1572 1573 1574 1575 1576 1577
group subset_thermostat id 1578 1579 1580 1581 1582 1583 1586 1587 1588 1589
group subset_thermostat id 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599
group subset_thermostat id 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611
group subset_thermostat id 1612 1613 1614 1615 1618 1619 1620 1621 1622 1623
group subset_thermostat id 1624 1625 1626 1627 1628 1629 1630 1631 1634 1635
group subset_thermostat id 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645
group subset_thermostat id 1646 1647 1650 1651 1652 1653 1654 1655 1656 1657
group subset_thermostat id 1658 1659 1660 1661 1662 1663 1666 1667 1668 1669
group subset_thermostat id 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679
group subset_thermostat id 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691
group subset_thermostat id 1692 1693 1694 1695 1698 1699 1700 1701 1702 1703
group subset_thermostat id 1704 1705 1706 1707 1708 1709 1710 1711 1714 1715
group subset_thermostat id 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725
group subset_thermostat id 1726 1727 1730 1731 1732 1733 1734 1735 1736 1737
group subset_thermostat id 1738 1739 1740 1741 1742 1743 1746 1747 1748 1749
group subset_thermostat id 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759
group subset_thermostat id 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771
group subset_thermostat id 1772 1773 1774 1775 1778 1779 1780 1781 1782 1783
group subset_thermostat id 1784 1785 1786 1787 1788 1789 1790 1791 1794 1795
group subset_thermostat id 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805
group subset_thermostat id 1806 1807 1810 1811 1812 1813 1814 1815 1816 1817
group subset_thermostat id 1818 1819 1820 1821 1822 1823 1826 1827 1828 1829
group subset_thermostat id 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839
group subset_thermostat id 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851
group subset_thermostat id 1852 1853 1854 1855 1858 1859 1860 1861 1862 1863
group subset_thermostat id 1864 1865 1866 1867 1868 1869 1870 1871 1874 1875
group subset_thermostat id 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885
group subset_thermostat id 1886 1887 1890 1891 1892 1893 1894 1895 1896 1897
group subset_thermostat id 1898 1899 1900 1901 1902 1903 1906 1907 1908 1909
group subset_thermostat id 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919
group subset_thermostat id 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931
group subset_thermostat id 1932 1933 1934 1935 1938 1939 1940 1941 1942 1943
group subset_thermostat id 1944 1945 1946 1947 1948 1949 1950 1951 1954 1955
group subset_thermostat id 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965
group subset_thermostat id 1966 1967 1970 1971 1972 1973 1974 1975 1976 1977
group subset_thermostat id 1978 1979 1980 1981 1982 1983 1986 1987 1988 1989
group subset_thermostat id 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999
group subset_thermostat id 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
group subset_thermostat id 2012 2013 2014 2015 2018 2019 2020 2021 2022 2023
group subset_thermostat id 2024 2025 2026 2027 2028 2029 2030 2031 2034 2035
group subset_thermostat id 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045
group subset_thermostat id 2046 2047 2050 2051 2052 2055 2056 2057 2060 2061
group subset_thermostat id 2062 2065 2066 2067 2070 2071 2072 2075 2076 2077
group subset_thermostat id 2080 2081 2082 2085 2086 2087 2090 2091 2092 2095
group subset_thermostat id 2096 2097 2100 2101 2102 2105 2106 2107 2110 2111
group subset_thermostat id 2112 2115 2116 2117 2120 2121 2122 2125 2126 2127
group subset_thermostat id 2130 2131 2132 2135 2136 2137 2140 2141 2142 2145
group subset_thermostat id 2146 2147 2150 2151 2152 2155 2156 2157 2160 2161
group subset_thermostat id 2162 2165 2166 2167 2170 2171 2172 2175 2176 2177
group subset_thermostat id 2180 2181 2182 2185 2186 2187 2190 2191 2192 2195
group subset_thermostat id 2196 2197 2200 2201 2202 2205 2206 2207 2210 2211
group subset_thermostat id 2212 2215 2216 2217 2220 2221 2222 2225 2226 2227
group subset_thermostat id 2230 2231 2232 2235 2236 2237 2240 2241 2242 2245
group subset_thermostat id 2246 2247 2250 2251 2252 2255 2256 2257 2260 2261
group subset_thermostat id 2262 2265 2266 2267 2270 2271 2272 2275 2276 2277
group subset_thermostat id 2280 2281 2282 2285 2286 2287 2290 2291 2292 2295
group subset_thermostat id 2296 2297 2300 2301 2302 2305 2306 2307 2310 2311
group subset_thermostat id 2312 2315 2316 2317 2320 2321 2322 2325 2326 2327
group subset_thermostat id 2330 2331 2332 2335 2336 2337 2340 2341 2342 2345
group subset_thermostat id 2346 2347 2350 2351 2352 2355 2356 2357 2360 2361
group subset_thermostat id 2362 2365 2366 2367 2370 2371 2372 2375 2376 2377
group subset_thermostat id 2380 2381 2382 2385 2386 2387 2390 2391 2392 2395
group subset_thermostat id 2396 2397 2400 2401 2402 2405 2406 2407 2410 2411
group subset_thermostat id 2412 2415 2416 2417 2420 2421 2422 2425 2426 2427
group subset_thermostat id 2430 2431 2432 2435 2436 2437 2440 2441 2442 2445
group subset_thermostat id 2446 2447 2450 2451 2452 2455 2456 2457 2460 2461
group subset_thermostat id 2462 2465 2466 2467 2470 2471 2472 2475 2476 2477
group subset_thermostat id 2480 2481 2482 2485 2486 2487 2490 2491 2492 2495
group subset_thermostat id 2496 2497 2500 2501 2502 2505 2506 2507 2510 2511
group subset_thermostat id 2512 2515 2516 2517 2520 2521 2522 2525 2526 2527
group subset_thermostat id 2530 2531 2532 2535 2536 2537 2540 2541 2542 2545
group subset_thermostat id 2546 2547 2550 2551 2552 2555 2556 2557 2560 2561
group subset_thermostat id 2562 2565 2566 2567 2570 2571 2572 2575 2576 2577
group subset_thermostat id 2580 2581 2582 2585 2586 2587 2590 2591 2592 2595
group subset_thermostat id 2596 2597 2600 2601 2602 2605 2606 2607 2610 2611
group subset_thermostat id 2612 2615 2616 2617 2620 2621 2622 2625 2626 2627
group subset_thermostat id 2630 2631 2632 2635 2636 2637 2640 2641 2642 2645
group subset_thermostat id 2646 2647 2650 2651 2652 2655 2656 2657 2660 2661
group subset_thermostat id 2662 2665 2666 2667 2670 2671 2672 2675 2676 2677
group subset_thermostat id 2680 2681 2682 2685 2686 2687 2690 2691 2692 2693
group subset_thermostat id 2694 2695 2696 2697 2698 2701 2702 2703 2704 2705
group subset_thermostat id 2706 2707 2708 2709 2712 2713 2714 2715 2716 2717
group subset_thermostat id 2718 2719 2720 2723 2724 2725 2726 2727 2728 2729
group subset_thermostat id 2730 2731 2734 2735 2736 2737 2738 2739 2740 2741
group subset_thermostat id 2742 2745 2746 2747 2748 2749 2750 2751 2752 2753
group subset_thermostat id 2756 2757 2758 2759 2760 2761 2762 2763 2764 2767
group subset_thermostat id 2768 2769 2770 2771 2772 2773 2774 2775 2778 2779
group subset_thermostat id 2780 2781 2782 2783 2784 2785 2786 2789 2790 2791
group subset_thermostat id 2792 2793 2794 2795 2796 2797 2800 2801 2802 2803
group subset_thermostat id 2804 2805 2806 2807 2808 2811 2812 2813 2814 2815
group subset_thermostat id 2816 2817 2818 2819 2822 2823 2824 2825 2826 2827
group subset_thermostat id 2828 2829 2830 2833 2834 2835 2836 2837 2838 2839
group subset_thermostat id 2840 2841 2844 2845 2846 2847 2848 2849 2850 2851
group subset_thermostat id 2852 2855 2856 2857 2858 2859 2860 2861 2862 2863
group subset_thermostat id 2866 2867 2868 2869 2870 2871 2872 2873 2874 2875
group subset_thermostat id 2876 2877 2878 2879 2882 2883 2884 2885 2886 2887
group subset_thermostat id 2888 2889 2890 2891 2892 2893 2894 2895 2898 2899
group subset_thermostat id 2900 2901 2902 2903 2904 2905 2906 2907 2908 2909
group subset_thermostat id 2910 2911 2914 2915 2916 2917 2918 2919 2920 2921
group subset_thermostat id 2922 2923 2924 2925 2926 2927 2930 2931 2932 2933
group subset_thermostat id 2934 2935 2936 2937 2938 2939 2940 2941 2942 2943
group subset_thermostat id 2946 2947 2948 2949 2950 2951 2952 2953 2954 2955
group subset_thermostat id 2956 2957 2958 2959 2962 2963 2964 2965 2966 2967
group subset_thermostat id 2968 2969 2970 2971 2972 2973 2974 2975 2978 2979
group subset_thermostat id 2980 2981 2982 2983 2984 2985 2986 2987 2988 2989
group subset_thermostat id 2990 2991 2994 2995 2996 2997 2998 2999 3000 3001
group subset_thermostat id 3002 3003 3004 3005 3006 3007 3010 3011 3012 3013
group subset_thermostat id 3014 3015 3016 3017 3018 3019 3020 3021 3022 3023
group subset_thermostat id 3026 3027 3028 3029 3030 3031 3032 3033 3034 3035
group subset_thermostat id 3036 3037 3038 3039 3042 3043 3044 3045 3046 3047
group subset_thermostat id 3048 3049 3050 3051 3052 3053 3054 3055 3058 3059
group subset_thermostat id 3060 3061 3062 3063 3064 3065 3066 3067 3068 3069
group subset_thermostat id 3070 3071 3074 3075 3076 3077 3078 3079 3080 3081
group subset_thermostat id 3082 3083 3084 3085 3086 3087 3090 3091 3092 3093
group subset_thermostat id 3094 3095 3096 3097 3098 3099 3100 3101 3102 3103
group subset_thermostat id 3106 3107 3108 3109 3110 3111 3112 3113 3114 3115
group subset_thermostat id 3116 3117 3118 3119 3122 3123 3124 3125 3126 3127
group subset_thermostat id 3128 3129 3130 3131 3132 3133 3134 3135 3138 3139
group subset_thermostat id 3140 3141 3142 3143 3144 3145 3146 3147 3148 3149
group subset_thermostat id 3150 3151 3154 3155 3156 3157 3158 3159 3160 3161
group subset_thermostat id 3162 3163 3164 3165 3166 3167 3170 3171 3172 3173
group subset_thermostat id 3174 3175 3176 3177 3178 3179 3180 3181 3182 3183
group subset_thermostat id 3186 3187 3188 3189 3190 3191 3192 3193 3194 3195
group subset_thermostat id 3196 3197 3198 3199 3202 3203 3204 3205 3206 3207
group subset_thermostat id 3208 3209 3210 3211 3212 3213 3214 3215 3218 3219
group subset_thermostat id 3220 3221 3222 3223 3224 3225 3226 3227 3228 3229
group subset_thermostat id 3230 3231 3234 3235 3236 3237 3238 3239 3240 3241
group subset_thermostat id 3242 3243 3244 3245 3246 3247 3250 3251 3252 3253
group subset_thermostat id 3254 3255 3256 3257 3258 3259 3260 3261 3262 3263
group subset_thermostat id 3266 3267 3268 3269 3270 3271 3272 3273 3274 3275
group subset_thermostat id 3276 3277 3278 3279 3282 3283 3284 3285 3286 3287
group subset_thermostat id 3288 3289 3290 3291 3292 3293 3294 3295 3298 3299
group subset_thermostat id 3300 3301 3302 3303 3304 3305 3306 3307 3308 3309
group subset_thermostat id 3310 3311 3314 3315 3316 3317 3318 3319 3320 3321
group subset_thermostat id 3322 3323 3324 3325 3326 3327 3330 3331 3332 3333
group subset_thermostat id 3334 3335 3336 3337 3338 3339 3340 3341 3342 3343
group subset_thermostat id 3346 3347 3348 3349 3350 3351 3352 3353 3354 3355
group subset_thermostat id 3356 3357 3358 3359 3362 3363 3364 3365 3366 3367
group subset_thermostat id 3368 3369 3370 3371 3372 3373 3374 3375 3378 3379
group subset_thermostat id 3380 3381 3382 3383 3384 3385 3386 3387 3388 3389
group subset_thermostat id 3390 3391 3394 3395 3396 3397 3398 3399 3400 3401
group subset_thermostat id 3402 3403 3404 3405 3406 3407 3410 3411 3412 3413
group subset_thermostat id 3414 3415 3416 3417 3418 3419 3420 3421 3422 3423
group subset_thermostat id 3426 3427 3428 3429 3430 3431 3432 3433 3434 3435
group subset_thermostat id 3436 3437 3438 3439 3442 3443 3444 3445 3446 3447
group subset_thermostat id 3448 3449 3450 3451 3452 3453 3454 3455 3458 3459
group subset_thermostat id 3460 3461 3462 3463 3464 3465 3466 3467 3468 3469
group subset_thermostat id 3470 3471 3474 3475 3476 3477 3478 3479 3480 3481
group subset_thermostat id 3482 3483 3484 3485 3486 3487 3490 3491 3492 3493
group subset_thermostat id 3494 3495 3496 3497 3498 3499 3500 3501 3502 3503
group subset_thermostat id 3506 3507 3508 3509 3510 3511 3512 3513 3514 3515
group subset_thermostat id 3516 3517 3518 3519 3522 3523 3524 3525 3526 3527
group subset_thermostat id 3528 3529 3530 3531 3532 3533 3534 3535 3538 3539
group subset_thermostat id 3540 3541 3542 3543 3544 3545 3546 3547 3548 3549
group subset_thermostat id 3550 3551 3554 3555 3556 3557 3558 3559 3560 3561
group subset_thermostat id 3562 3563 3564 3565 3566 3567 3570 3571 3572 3573
group subset_thermostat id 3574 3575 3576 3577 3578 3579 3580 3581 3582 3583
group subset_thermostat id 3586 3587 3588 3589 3590 3591 3592 3593 3594 3595
group subset_thermostat id 3596 3597 3598 3599 3602 3603 3604 3605 3606 3607
group subset_thermostat id 3608 3609 3610 3611 3612 3613 3614 3615 3618 3619
group subset_thermostat id 3620 3621 3622 3623 3624 3625 3626 3627 3628 3629
group subset_thermostat id 3630 3631 3634 3635 3636 3637 3638 3639 3640 3641
group subset_thermostat id 3642 3643 3644 3645 3646 3647 3650 3651 3652 3653
group subset_thermostat id 3654 3655 3656 3657 3658 3659 3660 3661 3662 3663
group subset_thermostat id 3666 3667 3668 3669 3670 3671 3672 3673 3674 3675
group subset_thermostat id 3676 3677 3678 3679 3682 3683 3684 3685 3686 3687
group subset_thermostat id 3688 3689 3690 3691 3692 3693 3694 3695 3698 3699
group subset_thermostat id 3700 3701 3702 3703 3704 3705 3706 3707 3708 3709
group subset_thermostat id 3710 3711 3714 3715 3716 3717 3718 3719 3720 3721
group subset_thermostat id 3722 3723 3724 3725 3726 3727 3730 3731 3732 3733
group subset_thermostat id 3734 3735 3736 3737 3738 3739 3740 3741 3742 3743
group subset_thermostat id 3746 3747 3748 3749 3750 3751 3752 3753 3754 3755
group subset_thermostat id 3756 3757 3758 3759 3762 3763 3764 3765 3766 3767
group subset_thermostat id 3768 3769 3770 3771 3772 3773 3774 3775 3778 3779
group subset_thermostat id 3780 3781 3782 3783 3784 3785 3786 3787 3788 3789
group subset_thermostat id 3790 3791 3794 3795 3796 3797 3798 3799 3800 3801
group subset_thermostat id 3802 3803 3804 3805 3806 3807 3810 3811 3812 3813
group subset_thermostat id 3814 3815 3816 3817 3818 3819 3820 3821 3822 3823
group subset_thermostat id 3826 3827 3828 3829 3830 3831 3832 3833 3834 3835
group subset_thermostat id 3836 3837 3838 3839 3842 3843 3844 3845 3846 3847
group subset_thermostat id 3848 3849 3850 3851 3852 3853 3854 3855 3858 3859
group subset_thermostat id 3860 3861 3862 3863 3864 3865 3866 3867 3868 3869
group subset_thermostat id 3870 3871 3874 3875 3876 3877 3878 3879 3880 3881
group subset_thermostat id 3882 3883 3884 3885 3886 3887 3890 3891 3892 3893
group subset_thermostat id 3894 3895 3896 3897 3898 3899 3900 3901 3902 3903
group subset_thermostat id 3906 3907 3908 3909 3910 3911 3912 3913 3914 3915
group subset_thermostat id 3916 3917 3918 3919 3922 3923 3924 3925 3926 3927
group subset_thermostat id 3928 3929 3930 3931 3932 3933 3934 3935 3938 3939
group subset_thermostat id 3940 3941 3942 3943 3944 3945 3946 3947 3948 3949
group subset_thermostat id 3950 3951 3954 3955 3956 3957 3958 3959 3960 3961
group subset_thermostat id 3962 3963 3964 3965 3966 3967 3970 3971 3972 3973
group subset_thermostat id 3974 3975 3976 3977 3978 3979 3980 3981 3982 3983
group subset_thermostat id 3986 3987 3988 3989 3990 3991 3992 3993 3994 3995
group subset_thermostat id 3996 3997 3998 3999 4002 4003 4004 4005 4006 4007
group subset_thermostat id 4008 4009 4010 4011 4012 4013 4014 4015 4018 4019
group subset_thermostat id 4020 4021 4022 4023 4024 4025 4026 4027 4028 4029
group subset_thermostat id 4030 4031 4034 4035 4036 4037 4038 4039 4040 4041
group subset_thermostat id 4042 4043 4044 4045 4046 4047 4050 4051 4052 4053
group subset_thermostat id 4054 4055 4056 4057 4058 4059 4060 4061 4062 4063
group subset_thermostat id 4066 4067 4068 4069 4070 4071 4072 4073 4074 4075
group subset_thermostat id 4076 4077 4078 4079 4082 4083 4084 4085 4086 4087
group subset_thermostat id 4088 4089 4090 4091 4092 4093 4094 4095 4098 4099
group subset_thermostat id 4100 4101 4102 4103 4104 4105 4106 4107 4108 4109
group subset_thermostat id 4110 4111 4114 4115 4116 4117 4118 4119 4120 4121
group subset_thermostat id 4122 4123 4124 4125 4126 4127 4130 4131 4132 4133
group subset_thermostat id 4134 4135 4136 4137 4138 4139 4140 4141 4142 4143
group subset_thermostat id 4146 4147 4148 4149 4150 4151 4152 4153 4154 4155
group subset_thermostat id 4156 4157 4158 4159 4162 4163 4164 4165 4166 4167
group subset_thermostat id 4168 4169 4170 4171 4172 4173 4174 4175 4178 4179
group subset_thermostat id 4180 4181 4182 4183 4184 4185 4186 4187 4188 4189
group subset_thermostat id 4190 4191 4194 4195 4196 4197 4198 4199 4200 4201
group subset_thermostat id 4202 4203 4204 4205 4206 4207 4210 4211 4212 4213
group subset_thermostat id 4214 4215 4216 4217 4218 4219 4220 4221 4222 4223
group subset_thermostat id 4226 4227 4228 4229 4230 4231 4232 4233 4234 4235
group subset_thermostat id 4236 4237 4238 4239 4242 4243 4244 4245 4246 4247
group subset_thermostat id 4248 4249 4250 4251 4252 4253 4254 4255 4258 4259
group subset_thermostat id 4260 4261 4262 4263 4264 4265 4266 4267 4268 4269
group subset_thermostat id 4270 4271 4274 4275 4276 4277 4278 4279 4280 4281
group subset_thermostat id 4282 4283 4284 4285 4286 4287 4290 4291 4292 4293
group subset_thermostat id 4294 4295 4296 4297 4298 4299 4300 4301 4302 4303
group subset_thermostat id 4306 4307 4308 4309 4310 4311 4312 4313 4314 4315
group subset_thermostat id 4316 4317 4318 4319 4322 4323 4324 4325 4326 4327
group subset_thermostat id 4328 4329 4330 4331 4332 4333 4334 4335 4338 4339
group subset_thermostat id 4340 4341 4342 4343 4344 4345 4346 4347 4348 4349
group subset_thermostat id 4350 4351 4354 4355 4356 4357 4358 4359 4360 4361
group subset_thermostat id 4362 4363 4364 4365 4366 4367 4370 4371 4372 4373
group subset_thermostat id 4374 4375 4376 4377 4378 4379 4380 4381 4382 4383
group subset_thermostat id 4386 4387 4388 4389 4390 4391 4392 4393 4394 4395
group subset_thermostat id 4396 4397 4398 4399 4402 4403 4404 4405 4406 4407
group subset_thermostat id 4408 4409 4410 4411 4412 4413 4414 4415 4418 4419
group subset_thermostat id 4420 4421 4422 4423 4424 4425 4426 4427 4428 4429
group subset_thermostat id 4430 4431 4434 4435 4436 4437 4438 4439 4440 4441
group subset_thermostat id 4442 4443 4444 4445 4446 4447 4450 4451 4452 4453
group subset_thermostat id 4454 4455 4456 4457 4458 4459 4460 4461 4462 4463
group subset_thermostat id 4466 4467 4468 4469 4470 4471 4472 4473 4474 4475
group subset_thermostat id 4476 4477 4478 4479 4482 4483 4484 4485 4486 4487
group subset_thermostat id 4488 4489 4490 4491 4492 4493 4494 4495 4498 4499
group subset_thermostat id 4500 4501 4502 4503 4504 4505 4506 4507 4508 4509
group subset_thermostat id 4510 4511 4514 4515 4516 4517 4518 4519 4520 4521
group subset_thermostat id 4522 4523 4524 4525 4526 4527 4530 4531 4532 4533
group subset_thermostat id 4534 4535 4536 4537 4538 4539 4540 4541 4542 4543
group subset_thermostat id 4546 4547 4548 4549 4550 4551 4552 4553 4554 4555
group subset_thermostat id 4556 4557 4558 4559 4562 4563 4564 4565 4566 4567
group subset_thermostat id 4568 4569 4570 4571 4572 4573 4574 4575 4578 4579
group subset_thermostat id 4580 4581 4582 4583 4584 4585 4586 4587 4588 4589
group subset_thermostat id 4590 4591 4594 4595 4596 4597 4598 4599 4600 4601
group subset_thermostat id 4602 4603 4604 4605 4606 4607 4610 4611 4612 4613
group subset_thermostat id 4614 4615 4616 4617 4618 4619 4620 4621 4622 4623
group subset_thermostat id 4626 4627 4628 4629 4630 4631 4632 4633 4634 4635
group subset_thermostat id 4636 4637 4638 4639 4642 4643 4644 4645 4646 4647
group subset_thermostat id 4648 4649 4650 4651 4652 4653 4654 4655
log 2.2_Velocities.out
#-------------------------------------------------------------------------------
# Stage 2.2: Set the initial velocities for $T
#-------------------------------------------------------------------------------
velocity movable create 300 72489 dist gaussian mom yes rot no
velocity fixed set 0.0 0.0 0.0
log 2.3_Deposition.out
#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 1000 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_N_atom id 4657
delete_atoms group deposition_atoms_N_atom
molecule depositing_species_N_atom deposition_N_atom.dat
region deposition_region_N_atom block EDGE EDGE EDGE EDGE 50 60 units box
region evaporation_region block EDGE EDGE EDGE EDGE 90 EDGE units box
group evaporation_group dynamic all region evaporation_region every 1000
uncompute thermo_temp
compute thermo_temp movable temp
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo ${Nthermo}
fix 1 movable nve
fix 2 evaporation_group reax/c/species 1 1 1000 removed_fragments.out element N Si terse yes
fix 3 all evaporate 1000 1000 evaporation_region 27657 molecule yes
fix dlan subset_thermostat langevin 300 300 20.0 59 tally yes
fix 4 movable ave/time 1 500000 500000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy f_dlan file 2.3_averages.txt off 1
fix 5 movable ave/time 50000000 1 50000000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy f_dlan file 2.3_instantaneous.txt
fix 6 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix deposition_N_atom_1 deposition_atoms_N_atom deposit 500 0 10000 27657 region deposition_region_N_atom mol depositing_species_N_atom vz -0.10564503102330547 -0.12912170458404001 vx 0.020697854830212851 -0.020697854830212851 vy 0.020697854830212851 -0.020697854830212851 near 1.50 id next units box
fix deposition_N_atom_2 deposition_atoms_N_atom nve
dump trj all custom 500000 2.3.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 500000 1 500000 v_etotal v_pe v_ke file 2.3.energies.txt
dump trj_N_atom deposition_atoms_N_atom custom 500000 2.3.trajectory_1.xyz id mol type q xs ys zs
timestep 0.2
run 5000000
write_dump all xyz final_2.3.xyz modify element N Si
undump trj
unfix trjE
undump trj_N_atom
write_dump deposition_atoms_N_atom custom 2.3.deposited_1.xyz id mol type q xs ys zs
restart 0
dump sci all custom 5000000 2.3.xyz id mol type q xs ys zs
run 0
undump sci
unfix 1
unfix 2
unfix 3
unfix 4
unfix 5
unfix 6
unfix deposition_N_atom_1
unfix deposition_N_atom_2
unfix dlan